User:Dima Golovenko/R.EcoRII

<!--

The line below this paragraph, containing "STRUCTURE_1na6", creates the "Structure Box" on the page.

You may change the PDB parameter (which sets the PDB file loaded into the applet)

or the SCENE parameter (which sets the initial scene displayed when the page is loaded),

or leave the SCENE parameter empty for the default display.

-->

{{STRUCTURE_1na6| PDB=1na6 | SCENE= }}

===Crystal structure of restriction endonuclease EcoRII mutant R88A===

<!--

The line below this paragraph, {{ABSTRACT_PUBMED_14659759}}, adds the Publication Abstract to the page

(as it appears on PubMed at http://www.pubmed.gov), where 14659759 is the PubMed ID number.

-->

{{ABSTRACT_PUBMED_14659759}}

==About this Structure==

1NA6 is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NA6 OCA].

[[Restriction endonuclease]] (REase) '''EcoRII''' (pronounced "eco R two") is an [[enzyme]] of [[restriction modification system]] (RM) naturally found in ''[[Escherichia coli]]'', a [[Gram-negative bacteria]]. Its [[molecular mass]] is 45.2 [[Atomic mass unit|kDa]], being composed of 402 [[amino acids]].<ref name="title">{{cite web | url = http://rebase.neb.com/rebase/enz/EcoRII.html | title = EcoRII | accessdate = 2008-03-23 | author = Richard J. Roberts | authorlink = | coauthors = | date = | format = | work = REBASE - The Restriction Enzyme Database | publisher = | pages = | language = | archiveurl = | archivedate = | quote = }}</ref>

==Mode of action==

EcoRII is a [[bacterial]] Type IIE<ref name="pmid12654995">{{cite journal | author = Roberts RJ, Belfort M, Bestor T, ''et al.'' | title = A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes | journal = Nucleic Acids Res. | volume = 31 | issue = 7 | pages = 1805–12 | year = 2003 | pmid = 12654995 | doi = 10.1093/nar/gkg274 | pmc = 152790 }} [http://nar.oxfordjournals.org/cgi/reprint/31/7/1805.pdf PDF] </ref> [[restriction endonuclease|REase]] that interacts with two<ref name="pmid10903314">{{cite journal | author = Mücke M, Lurz R, Mackeldanz P, Behlke J, Krüger DH, Reuter M | title = Imaging DNA loops induced by restriction endonuclease EcoRII. A single amino acid substitution uncouples target recognition from cooperative DNA interaction and cleavage | journal = J. Biol. Chem. | volume = 275 | issue = 39 | pages = 30631–7 | year = 2000 | pmid = 10903314 | doi = 10.1074/jbc.M003904200 }}[http://www.jbc.org/cgi/reprint/275/39/30631.pdf PDF]</ref> or [http://pubs.acs.org/isubscribe/journals/bichaw/46/i39/figures/bi701123un00001.gif three]<ref name="pmid17845057">{{cite journal | author = Shlyakhtenko LS, Gilmore J, Portillo A, Tamulaitis G, Siksnys V, Lyubchenko YL | title = Direct visualization of the EcoRII-DNA triple synaptic complex by atomic force microscopy | journal = Biochemistry | volume = 46 | issue = 39 | pages = 11128–36 | year = 2007 | pmid = 17845057 | doi = 10.1021/bi701123u }}</ref> copies of the pseudopalindromic [[dsDNA|DNA]] [[Restriction_enzyme#Recognition_site|recognition sequence]] [[5' end|5']]-[[Cytosine|CC]]W[[Guanine|GG]]-[[3' end|3']] ([[W]] = [[Adenine|A]] or [[Thymine|T]]), one being the actual target of cleavage, the other(s) serving as the [[Allosteric regulation#Allosteric activation and inhibition|allosteric activator]](s). EcoRII cut target [[dsDNA|DNA]] sequence CCWGG generating [[sticky ends]].<ref name="isbn0-7167-3520-2">{{cite book | author = Griffiths, Anthony J. F. | title = An Introduction to genetic analysis | publisher = W.H. Freeman | location = San Francisco | year = 1999 | pages = | isbn = 0-7167-3520-2 | oclc = | doi = }}</ref>

==Cut diagram==

{| class="wikitable"

| Recognition site

| Cut results

|-

|

5' NN'''CCWGG'''NN

3' NN'''GGWCC'''NN

|

5' NN '''CCWGG'''NN

3' NN'''GGWCC''' NN

|}

==Structure==

The [[apo]] [[X-ray crystallography|crystal]] [[protein structure|structure]] of EcoRII [[Point mutation|mutant]] R88A ({{PDB|1NA6}})<ref name="Zhou_2004">{{cite journal | author = Zhou XE, Wang Y, Reuter M, Mücke M, Krüger DH, Meehan EJ, Chen L | title = Crystal structure of type IIE restriction endonuclease EcoRII reveals an autoinhibition mechanism by a novel effector-binding fold | journal = J. Mol. Biol. | volume = 335 | issue = 1 | pages = 307–19 | year = 2004 | pmid = 14659759 | doi = 10.1016/j.jmb.2003.10.030 }}</ref> has been solved at 2.1 [[Å]] [[Resolution (electron density)|resolution]]. The EcoRII [[Primary structure|monomer]] has two [[Protein domains|domains]], [[N-terminus|N-terminal]] and [[C-terminus|C-terminal]], linked through a [[hinge]] [[turn (biochemistry)|loop]].

===Effector-binding domain===

* <scene name='User:Dima_Golovenko/R.EcoRII/Effector_domain/1'>The N-terminal</scene> [[Effector (biology)|effector]]-[[DNA-binding domain|binding domain]] has a archetypal DNA-binding pseudobarrel fold ({{SCOP|101936}}) with a prominent [[structural motif|cleft]]. [[Structural alignment#DALI|Structural superposition]] showed it is evolutionarily related to:

*[[B3 DNA binding domain]] ({{SCOP|117343}}) from the [[transcription factors]] in [[higher plants]] ({{PDB|1WID}})<ref name="pmid15548737">{{cite journal | author = Yamasaki K, Kigawa T, Inoue M, Tateno M, Yamasaki T, Yabuki T, Aoki M, Seki E, Matsuda T, Tomo Y, Hayami N, Terada T, Shirouzu M, Osanai T, Tanaka A, Seki M, Shinozaki K, Yokoyama S | title = Solution structure of the B3 DNA binding domain of the Arabidopsis cold-responsive transcription factor RAV1 | journal = Plant Cell | volume = 16 | issue = 12 | pages = 3448–59 | year = 2004 | pmid = 15548737 | doi = 10.1105/tpc.104.026112 | pmc = 535885 }}[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=535885&blobtype=pdf PDF]</ref>

*C-terminal domain of [[restriction endonuclease]] BfiI<ref name="BfiI">{{cite web | url = http://rebase.neb.com/rebase/enz/BfiI.html | title = BfiI | accessdate = 2008-03-23 | author = Richard J. Roberts | authorlink = | coauthors = | date = | format = | work = REBASE - The Restriction Enzyme Database | publisher = | pages = | language = | archiveurl = | archivedate = | quote = }}</ref> ({{PDB|2C1L}})<ref name="pmid16247004">{{cite journal | author = Grazulis S, Manakova E, Roessle M, Bochtler M, Tamulaitiene G, Huber R, Siksnys V | title = Structure of the metal-independent restriction enzyme BfiI reveals fusion of a specific DNA-binding domain with a nonspecific nuclease | journal = Proc. Natl. Acad. Sci. U.S.A. | volume = 102 | issue = 44 | pages = 15797–802 | year = 2005 | pmid = 16247004 | doi = 10.1073/pnas.0507949102 | pmc = 1266039 }} [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1266039&blobtype=pdf PDF]</ref>

===Catalytic domain===

<scene name='User:Dima_Golovenko/R.EcoRII/Catalytic_domain/1'>The catalytic domain</scene> has a typical<ref name="pmid17369272">{{cite journal | author = Niv MY, Ripoll DR, Vila JA, Liwo A, Vanamee ES, Aggarwal AK, Weinstein H, Scheraga HA | title = Topology of Type II REases revisited; structural classes and the common conserved core | journal = NAR | volume = 35 | issue = 7 | pages = 2227–37 | year = 2007 | pmid = 17369272 | doi = 10.1093/nar/gkm045 | pmc = 1874628}} [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1874628&blobtype=pdf PDF]</ref> restriction endonuclease-like fold ({{SCOP|52979}}) and belongs to the large (more than 30 members) [[restriction endonuclease]] superfamily ({{SCOP|52980}}).

==Autoinhibition/activation mechanism==

[[Structural alignment#Structural_superposition|Structure-based sequence]] alignment and [[site-directed mutagenesis]] identified the putative PD..D/EXK [[active site]]s of the EcoRII catalytic domain dimer that in apo structure are spatially blocked by the N-terminal domains.<ref name="Zhou_2004"/>

==See also==

*[[EcoRI]], another nuclease enzyme from ''[[Escherichia coli]]''.

*[[EcoRV]], another nuclease enzyme from ''[[Escherichia coli]]''.

*[[B3 DNA binding domain]] from [[higher plants]] is evolutionary related to EcoRII

<!-- *[[BamHI]], another nuclease enzyme from ''[[Bacillus amyloliquefaciens]]''.

*[[HindIII]], another nuclease enzyme from ''[[Haemophilus influenzae]]''.

*[[HaeIII]], another nuclease enzyme from ''[[Haemophilus aegyptius]]''.

*[[TaqI]], another nuclease enzyme from ''[[Thermus aquaticus]]''. -->

*[[FokI]], another nuclease enzyme from ''[[Flavobacterium okeanokoites]]''

==External links==

*EcoRII in Restriction Enzyme Database [http://rebase.neb.com/rebase/enz/EcoRII.html REBASE]

<!-- *EcoRII from [http://www.fermentas.com/catalog/re/ecorii.htm Fermentas] -->

==References==

{{Reflist|2}}

<references/>

==Reference==

<ref group="xtra">PMID:14659759</ref><references group="xtra"/>

[[Category: Escherichia coli]]

[[Category: Type II site-specific deoxyribonuclease]]

[[Category: Chen, L.]]announced

[[Category: Kruger, D H.]]

[[Category: Meehan, E J.]]

[[Category: Mucke, M.]]

[[Category: Reuter, M.]]

[[Category: Wang, Y.]]

[[Category: Zhou, X E.]]

[[Category: Mutation]]

[[Category: Replication]]

[[Category: Site-specific restriction]]

''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 03:36:10 2009''